Package | Description |
---|---|
com.compomics.cli.fasta | |
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
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com.compomics.util.experiment.identification.utils | |
com.compomics.util.experiment.io.biology.protein |
Experiment IO classes for biological resources.
|
com.compomics.util.experiment.io.biology.protein.converters |
Fasta file converters.
|
com.compomics.util.gui.parameters.identification.search |
Dialogs for searh parameters.
|
com.compomics.util.parameters.identification.advanced |
Advanced Identification parameters.
|
com.compomics.util.parameters.identification.search |
Identification parameters relative to the search.
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Modifier and Type | Method and Description |
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FastaParameters |
FastaParametersInputBean.getFastaParameters()
Returns the fasta parameters as parsed from the command line.
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Constructor and Description |
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FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
ModificationParameters modificationSettings,
PeptideVariantsParameters peptideVariantsPreferences)
Constructor.
|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
PeptideVariantsParameters peptideVariantsPreferences,
SearchParameters searchParameters)
Constructor.
|
Modifier and Type | Method and Description |
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static boolean |
ProteinUtils.isDecoy(String accession,
FastaParameters fastaParameters)
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given fasta parameters.
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Modifier and Type | Method and Description |
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static FastaParameters |
FastaParameters.inferParameters(File fastaFile)
Infers the parameters used to parse the file.
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static FastaParameters |
FastaParameters.inferParameters(File fastaFile,
WaitingHandler waitingHandler)
Infers the parameters used to parse the file.
|
Modifier and Type | Method and Description |
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static FastaSummary |
FastaSummary.getSummary(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler)
Gathers summary data on the fasta file content.
|
boolean |
FastaParameters.isSameAs(FastaParameters fastaParameters)
Returns a boolean indicating whether the parsing parameters are the same as the given parameters.
|
Modifier and Type | Method and Description |
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static FastaParameters |
DecoyConverter.getDecoyParameters(FastaParameters targetParameters)
Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.
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Modifier and Type | Method and Description |
---|---|
static FastaParameters |
DecoyConverter.getDecoyParameters(FastaParameters targetParameters)
Returns the FASTA parameters of the target-decoy database based on the parameters of the target database.
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Modifier and Type | Method and Description |
---|---|
FastaParameters |
SequenceDbDetailsDialog.getFastaParameters()
Returns the fasta parameters.
|
Constructor and Description |
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SequenceDbDetailsDialog(Dialog owner,
Frame parent,
File selectedFastaFile,
FastaParameters fastaParameters,
LastSelectedFolder lastSelectedFolder,
boolean dbEditable,
Image normalImange,
Image waitingImage)
Creates a new SequenceDbDetailsDialog with a dialog as owner.
|
SequenceDbDetailsDialog(Frame parent,
File selectedFastaFile,
FastaParameters fastaParameters,
LastSelectedFolder lastSelectedFolder,
boolean dbEditable,
Image normalImange,
Image waitingImage)
Creates a new SequenceDbDetailsDialog.
|
Modifier and Type | Method and Description |
---|---|
FastaParameters |
ProteinInferenceParameters.getFastaParameters()
Returns the parameters to use to parse the fasta file.
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinInferenceParameters.setFastaParameters(FastaParameters fastaParameters)
Sets the parameters to use to parse the fasta file.
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Modifier and Type | Method and Description |
---|---|
FastaParameters |
SearchParameters.getFastaParameters()
Returns the parameters to use to parse the fasta file.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchParameters.setFastaParameters(FastaParameters fastaParameters)
Sets the parameters to use to parse the fasta file.
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